Prerequisites/Recommended Background

Class Meetings & Attendance

Tuesdays 8:00 AM – 12:00 PM, Seaver 120

This is a hands-on laboratory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructor should be notified as soon as possible, electronically or by phone, of the reasons for all absences. LMU has published H1N1 flu prevention guidelines that are applicable to this course: http://www.lmu.edu/resources/emergency/status/H1N1.htm

Mutual Responsibilities

This course is designed to foster your development as a scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructor is to provide the expert coaching to support and assist you on your journey. All of the laboratory exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

Classroom and Laboratory Environment

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

You are responsible for your own learning and for being a good class citizen.

We will act with honesty and integrity at all times.

We will always treat individuals with respect.

Class will start promptly on time.

You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.

You are expected to bring the required materials to each class session.

Cell phones, pagers, and other communication or music devices will be turned off.

Course Web Site

This is the course web site. You will need to register with OpenWetware.org to be able to edit the wiki and complete coursework. I will post updates to the course schedule and electronic copies of all handouts, assignments, and readings on that site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in BIOL 398-01 on MyLMUConnect (formerly known as Blackboard). The MyLMUConnect site may be used for materials that cannot be made public on the OpenWetware.org wiki.

Required Texts

Specific readings are given on the schedule and may be revised. Readings will also be assigned from other sources and will be posted on the course web site or put on reserve in the library.

Required Materials (must be brought to each class meeting)

3-ring binder with all course handouts

Pen, pencil, extra paper

USB flash drive to store bioinformatics data (the more memory the better)

Course Description

Bioinformatics is the application of information technology (informatics) to biological data. Informatics is the representation, organization, manipulation, distribution, maintenance, and use of digital information. When applied to biological data, informatics provides databases and analytical tools for answering biological questions. Bioinformatics is inherently interdisciplinary, involving aspects of biology, computer science, mathematics, physics, and chemistry. While computers have been used to analyze biological data since their invention, the need for computational methods has recently exploded due to the huge amounts of data produced by genome sequencing projects and other high-throughput technologies. Bioinformatics techniques are being used to move the field of biology from a “one gene at a time” approach, to the analysis of whole systems. In this course, students will learn current bioinformatics techniques to address systems-level biological questions. Topics include sequence alignment and phylogeny, protein structural biology, and the analysis of DNA microarray data.

Course Objectives and Learning Outcomes

To understand how biological information is encoded in the genome and to apply this knowledge to a variety of biological tasks and problems

To become a bioinformatics tool “power user” by practicing the skills of computer literacy and learning the following about each bioinformatics technique we use:

what biological questions is the technique used to answer?

how does the technique work?

how do you perform the technique?

what are the limitations of the technique?

To read and critically evaluate the primary scientific literature

To form opinions about the ethical, legal, and social implications of bioinformatics research consistent with your values

To be confident in "leaving your comfort zone", flourishing outside of it, and learning more about bioinformatics on your own

Final course grading scale

Electronic Laboratory Notebook

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. The bioinformatics equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice the documentation skills needed by users of bioinformatics tools by keeping an electronic lab notebook or journal. The technology we will use is a public MediaWiki site hosted by OpenWetware.org, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructor will read and grade. You will use the OpenWetware site to complete the assignments as well. The following guidelines apply:

Your weekly journal entry is due every midnight on Monday PST (Sunday night/Monday morning). Note that the OpenWetware server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00 on the server.

You will earn 10 points per weekly submission. Late journal entries will be accepted up to one week later for up to half credit.

The instructor will read and comment on how to improve your journal entries.

Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.

Generally, your journal entries will consist of:

Workflow and other documentation for hands-on exercises and projects

Answers to any specific questions posed in the exercise

Reflection on your learning

Journal Club and Ethical Case Study Presentations

Each bioinformatics project will begin with a "Journal Club" where students will present and lead discussion of research articles from the primary literature. In addition, we may also discuss ethical case studies relating to the topics in the course. Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations and ethics case studies will not be accepted.

Oral Lab Reports

The final step in the scientific method is communication of the results to the scientific community. In bioinformatics, the communication takes place in the form of peer-reviewed papers, presentations and posters at conferences, and through web sites. To build your scientific communication skills, you will give an oral lab report for each of the bioinformatics projects assigned in the course. Because that day’s class content is dependent upon each student being ready to give his or her presentation, late oral lab reports will not be accepted.

Extra Credit

Students may accumulate up to 2.5% of their final grade in extra credit by attending Biology Department seminars and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. Students arriving late to the seminar will not be granted credit—so don’t be late!

Certain, non-Biology Department seminars may be approved in advance for extra credit at the instructor’s discretion. To receive credit for these non-Biology Department seminars, you must turn in a one-page summary of the seminar within one week of the date of the seminar or they will not count as extra credit.

Special Accommodations

Students with special needs who need reasonable modifications, special assistance, or accommodations in this course (such as a documented disability [physical, learning, or psychological]) should contact the Disability Services Office (Daum Hall, Room 224, x84535, http://www.lmu.edu/dss) as early in the semester as possible. All discussions will remain confidential. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

Revision Notice

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this course web site at http://www.openwetware.org/wiki/BIOL398-01/S10.